On 12/25/2011 7:56 PM, Ashalatha Sreshty wrote:
Dear All,
I have a problem running gromacs for a oligosaccharide. it has 14
units sugars containing glucose, mannose and N-acetyl glucosamine
units. I want to do MD simulations for this with opls aa force field.
For this I have generated the .itp files using topolgen (edited the
atoms according to the opls atoms types) but when I am executing
grompp command the following error comes up:
ERROR 226 [file 901opls.itp, line 2897]:
No default Ryckaert-Bell. types
The R-B dihedral defined on line 2897 does not have parameters
associated with it on that line, and grompp could find none for the atom
types involved back in the [dihedraltypes] section of the force field.
You'll have to do some detective work to find out why.
ERROR 227 [file 901opls.itp, line 2902]:
No default Ryckaert-Bell. types
ERROR 228 [file 901opls.itp, line 2903]:
No default Ryckaert-Bell. types
ERROR 229 [file 901opls.itp, line 2904]:
No default Ryckaert-Bell. types
Excluding 3 bonded neighbours molecule type 'DRG'
NOTE 1 [file 901opls.top, line 19]:
System has non-zero total charge: -2.177100e+01
You have a net charge of -21.771, so your topologies are mangled somehow.
Mark
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
There was 1 note
------------------------------
-------------------------
Program grompp_d, VERSION 4.0.5
Source code file: grompp.c, line: 986
Fatal error:
There were 229 errors in input file(s)
These are the lines of the dihedrals in .itp file
I do not understand what to do next. Please help me resolve this problem
and also educate me how to assign opls forcefield to carbohydrates for
MD simulations. Thank you in advance.
AshaLatha Sreshty
Molecular Sciences Laboratory
National Institute of Immunology
New Delhi, India
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